1 |
#include <cstdlib> |
2 |
#include <cstdio> |
3 |
#include <cstring> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#include "ForceFields.hpp" |
9 |
#include "SRI.hpp" |
10 |
#include "simError.h" |
11 |
|
12 |
|
13 |
// Declare the structures that will be passed by the parser and MPI |
14 |
|
15 |
typedef struct{ |
16 |
char name[15]; |
17 |
double mass; |
18 |
double epslon; |
19 |
double sigma; |
20 |
int ident; |
21 |
int last; // 0 -> default |
22 |
// 1 -> in MPI: tells nodes to stop listening |
23 |
} atomStruct; |
24 |
|
25 |
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ); |
26 |
|
27 |
#ifdef IS_MPI |
28 |
|
29 |
#include "mpiForceField.h" |
30 |
|
31 |
MPI_Datatype mpiAtomStructType; |
32 |
|
33 |
#endif |
34 |
|
35 |
|
36 |
// declaration of functions needed to wrap the fortran module |
37 |
|
38 |
extern "C" { |
39 |
void forcefactory_( char* forceName, |
40 |
int* status, |
41 |
void (*wrapFunction)( void (*p1)( int* ident, |
42 |
double* mass, |
43 |
double* epslon, |
44 |
double* sigma, |
45 |
int* status ), |
46 |
void (*p2)( void ), |
47 |
void (*p3)( double* positionArray, |
48 |
double* forceArray, |
49 |
double* potentialEnergy, |
50 |
short int* doPotentialCalc )), |
51 |
int forceNameLength ); |
52 |
} |
53 |
|
54 |
|
55 |
void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
56 |
double* sigma, int* status ), |
57 |
void (*p2)( void ), |
58 |
void (*p3)( double* positionArray,double* forceArray, |
59 |
double* potentialEnergy, |
60 |
short int* doPotentialCalc ) ); |
61 |
|
62 |
void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma, |
63 |
int* status ); |
64 |
|
65 |
void (*initLJfortran)( void ); |
66 |
|
67 |
LJ_FF* currentLJwrap; |
68 |
|
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|
70 |
//**************************************************************** |
71 |
// begins the actual forcefield stuff. |
72 |
//**************************************************************** |
73 |
|
74 |
LJ_FF::LJ_FF(){ |
75 |
|
76 |
char fileName[200]; |
77 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
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char* ffPath; |
79 |
char temp[200]; |
80 |
char errMsg[1000]; |
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|
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// do the funtion wrapping |
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currentLJwrap = this; |
84 |
wrapMe(); |
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|
86 |
#ifdef IS_MPI |
87 |
int i; |
88 |
|
89 |
// ********************************************************************** |
90 |
// Init the atomStruct mpi type |
91 |
|
92 |
atomStruct atomProto; // mpiPrototype |
93 |
int atomBC[3] = {15,3,2}; // block counts |
94 |
MPI_Aint atomDspls[3]; // displacements |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
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|
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MPI_Address(&atomProto.name, &atomDspls[0]); |
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MPI_Address(&atomProto.mass, &atomDspls[1]); |
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MPI_Address(&atomProto.ident, &atomDspls[2]); |
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|
101 |
atomMbrTypes[0] = MPI_CHAR; |
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atomMbrTypes[1] = MPI_DOUBLE; |
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atomMbrTypes[2] = MPI_INT; |
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|
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for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
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|
107 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
108 |
MPI_Type_commit(&mpiAtomStructType); |
109 |
|
110 |
// *********************************************************************** |
111 |
|
112 |
if( worldRank == 0 ){ |
113 |
#endif |
114 |
|
115 |
// generate the force file name |
116 |
|
117 |
strcpy( fileName, "LJ_FF.frc" ); |
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// fprintf( stderr,"Trying to open %s\n", fileName ); |
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|
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// attempt to open the file in the current directory first. |
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|
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frcFile = fopen( fileName, "r" ); |
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|
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if( frcFile == NULL ){ |
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|
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// next see if the force path enviorment variable is set |
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|
128 |
ffPath = getenv( ffPath_env ); |
129 |
if( ffPath == NULL ) { |
130 |
sprintf( painCave.errMsg, |
131 |
"Error opening the force field parameter file: %s\n" |
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"Have you tried setting the FORCE_PARAM_PATH environment " |
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"vairable?\n", |
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fileName ); |
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painCave.isFatal = 1; |
136 |
simError(); |
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} |
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|
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|
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strcpy( temp, ffPath ); |
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strcat( temp, "/" ); |
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strcat( temp, fileName ); |
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strcpy( fileName, temp ); |
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|
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frcFile = fopen( fileName, "r" ); |
146 |
|
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if( frcFile == NULL ){ |
148 |
|
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sprintf( painCave.errMsg, |
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"Error opening the force field parameter file: %s\n" |
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"Have you tried setting the FORCE_PARAM_PATH environment " |
152 |
"vairable?\n", |
153 |
fileName ); |
154 |
painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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#ifdef IS_MPI |
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} |
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|
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sprintf( checkPointMsg, "LJ_FF file opened sucessfully." ); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
166 |
} |
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|
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|
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LJ_FF::~LJ_FF(){ |
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|
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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|
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fclose( frcFile ); |
176 |
|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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|
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void LJ_FF::wrapMe( void ){ |
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|
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char* currentFF = "LJ"; |
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int isError = 0; |
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|
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forcefactory_( currentFF, &isError, LJfunctionWrapper, strlen(currentFF) ); |
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|
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if( isError ){ |
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|
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sprintf( painCave.errMsg, |
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"LJ_FF error: an error was returned from fortran when the " |
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"the functions were being wrapped.\n" ); |
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painCave.isFatal = 1; |
196 |
simError(); |
197 |
} |
198 |
|
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#ifdef IS_MPI |
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sprintf( checkPointMsg, "LJ_FF functions succesfully wrapped." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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|
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|
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void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
207 |
double* sigma, int* status ), |
208 |
void (*p2)( void ), |
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void (*p3)( double* positionArray,double* forceArray, |
210 |
double* potentialEnergy, |
211 |
short int* doPotentialCalc ) ){ |
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|
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|
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p1 = newLJtype; |
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p2 = initLJfortran; |
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this->setLJfortran( p3 ); |
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} |
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|
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|
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|
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void LJ_FF::initializeAtoms( void ){ |
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|
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class LinkedType { |
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public: |
225 |
LinkedType(){ |
226 |
next = NULL; |
227 |
name[0] = '\0'; |
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} |
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~LinkedType(){ if( next != NULL ) delete next; } |
230 |
|
231 |
LinkedType* find(char* key){ |
232 |
if( !strcmp(name, key) ) return this; |
233 |
if( next != NULL ) return next->find(key); |
234 |
return NULL; |
235 |
} |
236 |
|
237 |
|
238 |
void add( atomStruct &info ){ |
239 |
|
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// check for duplicates |
241 |
|
242 |
if( !strcmp( info.name, name ) ){ |
243 |
sprintf( simError.painCave, |
244 |
"Duplicate LJ atom type \"%s\" found in " |
245 |
"the LJ_FF param file./n", |
246 |
name ); |
247 |
painCave.isFatal = 1; |
248 |
simError(); |
249 |
} |
250 |
|
251 |
if( next != NULL ) next->add(info); |
252 |
else{ |
253 |
next = new LinkedType(); |
254 |
strcpy(next->name, info.name); |
255 |
next->mass = info.mass; |
256 |
next->epslon = info.epslon; |
257 |
next->sigma = info.sigma; |
258 |
next->ident = info.ident; |
259 |
} |
260 |
} |
261 |
|
262 |
|
263 |
#ifdef IS_MPI |
264 |
|
265 |
void duplicate( atomStruct &info ){ |
266 |
strcpy(info.name, name); |
267 |
info.mass = mass; |
268 |
info.epslon = epslon; |
269 |
info.sigma = sigma; |
270 |
info.ident = ident; |
271 |
info.last = 0; |
272 |
} |
273 |
|
274 |
|
275 |
#endif |
276 |
|
277 |
char name[15]; |
278 |
double mass; |
279 |
double epslon; |
280 |
double sigma; |
281 |
int ident; |
282 |
LinkedType* next; |
283 |
}; |
284 |
|
285 |
LinkedType* headAtomType; |
286 |
LinkedType* currentAtomType; |
287 |
atomStruct info; |
288 |
info.last = 1; // initialize last to have the last set. |
289 |
// if things go well, last will be set to 0 |
290 |
|
291 |
int i; |
292 |
int identNum; |
293 |
|
294 |
Atom** the_atoms; |
295 |
int nAtoms; |
296 |
the_atoms = entry_plug->atoms; |
297 |
nAtoms = entry_plug->n_atoms; |
298 |
|
299 |
|
300 |
#ifdef IS_MPI |
301 |
if( worldRank == 0 ){ |
302 |
#endif |
303 |
|
304 |
// read in the atom types. |
305 |
|
306 |
headAtomType = new LinkedType; |
307 |
|
308 |
fastFoward( "AtomTypes", "initializeAtoms" ); |
309 |
|
310 |
// we are now at the AtomTypes section. |
311 |
|
312 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
313 |
lineNum++; |
314 |
|
315 |
|
316 |
// read a line, and start parseing out the atom types |
317 |
|
318 |
if( eof_test == NULL ){ |
319 |
sprintf( painCave.errMsg, |
320 |
"Error in reading Atoms from force file at line %d.\n", |
321 |
lineNum ); |
322 |
painCave.isFatal = 1; |
323 |
simError(); |
324 |
} |
325 |
|
326 |
identNum = 1; |
327 |
// stop reading at end of file, or at next section |
328 |
while( readLine[0] != '#' && eof_test != NULL ){ |
329 |
|
330 |
// toss comment lines |
331 |
if( readLine[0] != '!' ){ |
332 |
|
333 |
// the parser returns 0 if the line was blank |
334 |
if( parseAtomLJ( readLine, lineNum, info ) ){ |
335 |
info.ident = identNum; |
336 |
headAtomType->add( info );; |
337 |
identNum++; |
338 |
} |
339 |
} |
340 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
341 |
lineNum++; |
342 |
} |
343 |
|
344 |
#ifdef IS_MPI |
345 |
|
346 |
// send out the linked list to all the other processes |
347 |
|
348 |
sprintf( checkPointMsg, |
349 |
"LJ_FF atom structures read successfully." ); |
350 |
MPIcheckPoint(); |
351 |
|
352 |
currentAtomType = headAtomType; |
353 |
while( currentAtomType != NULL ){ |
354 |
currentAtomType->duplicate( info ); |
355 |
sendFrcStruct( &info, mpiAtomStructType ); |
356 |
currentAtomType = currentAtomType->next; |
357 |
} |
358 |
info.last = 1; |
359 |
sendFrcStruct( &info, mpiAtomStructType ); |
360 |
|
361 |
} |
362 |
|
363 |
else{ |
364 |
|
365 |
// listen for node 0 to send out the force params |
366 |
|
367 |
MPIcheckPoint(); |
368 |
|
369 |
headAtomType = new LinkedType; |
370 |
recieveFrcStruct( &info, mpiAtomStructType ); |
371 |
while( !info.last ){ |
372 |
|
373 |
headAtomType->add( info ); |
374 |
recieveFrcStruct( &info, mpiAtomStructType ); |
375 |
} |
376 |
} |
377 |
#endif // is_mpi |
378 |
|
379 |
// call new A_types in fortran |
380 |
|
381 |
int isError; |
382 |
currentAtomType = headAtomType; |
383 |
while( currentAtomType != NULL ){ |
384 |
|
385 |
if( currentAtomType->name[0] != NULL ){ |
386 |
isError = 0; |
387 |
newLJtype( &(currentAtomType->ident), |
388 |
&(currentAtomType->mass), |
389 |
&(currentAtomType->epslon), |
390 |
&(currentAtomType->sigma), |
391 |
isError ); |
392 |
if( isError ){ |
393 |
sprintf( painCave.errMsg, |
394 |
"Error initializing the \"%s\" atom type in fortran\n", |
395 |
currentAtomType->name ); |
396 |
painCave.isFatal = 1; |
397 |
simError(); |
398 |
} |
399 |
} |
400 |
currentAtomType = currentAtomType->next; |
401 |
} |
402 |
|
403 |
#ifdef IS_MPI |
404 |
sprintf( checkPointMsg, |
405 |
"LJ_FF atom structures successfully sent to fortran\n" ); |
406 |
MPIcheckPoint(); |
407 |
#endif // is_mpi |
408 |
|
409 |
|
410 |
|
411 |
// initialize the atoms |
412 |
|
413 |
Atom* thisAtom; |
414 |
|
415 |
for( i=0; i<nAtoms; i++ ){ |
416 |
|
417 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
418 |
if( currentAtomType == NULL ){ |
419 |
sprintf( painCave.errMsg, |
420 |
"AtomType error, %s not found in force file.\n", |
421 |
the_atoms[i]->getType() ); |
422 |
painCave.isFatal = 1; |
423 |
simError(); |
424 |
} |
425 |
|
426 |
the_atoms[i]->setMass( currentAtomType->mass ); |
427 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
428 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
429 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
430 |
the_atoms[i]->setLJ(); |
431 |
} |
432 |
|
433 |
|
434 |
// clean up the memory |
435 |
|
436 |
delete headAtomType; |
437 |
|
438 |
#ifdef IS_MPI |
439 |
sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" ); |
440 |
MPIcheckPoint(); |
441 |
#endif // is_mpi |
442 |
|
443 |
} |
444 |
|
445 |
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
446 |
|
447 |
if( entry_plug->n_bonds ){ |
448 |
sprintf( painCave.errMsg, |
449 |
"LJ_FF does not support bonds.\n" ); |
450 |
painCave.isFatal = 1; |
451 |
simError(); |
452 |
} |
453 |
#ifdef IS_MPI |
454 |
MPIcheckPoint(); |
455 |
#endif // is_mpi |
456 |
|
457 |
} |
458 |
|
459 |
void LJ_FF::initializeBends( bend_set* the_bends ){ |
460 |
|
461 |
if( entry_plug->n_bends ){ |
462 |
sprintf( painCave.errMsg, |
463 |
"LJ_FF does not support bends.\n" ); |
464 |
painCave.isFatal = 1; |
465 |
simError(); |
466 |
} |
467 |
#ifdef IS_MPI |
468 |
MPIcheckPoint(); |
469 |
#endif // is_mpi |
470 |
|
471 |
} |
472 |
|
473 |
void LJ_FF::initializeTorsions( torsion_set* the_torsions ){ |
474 |
|
475 |
if( entry_plug->n_torsions ){ |
476 |
sprintf( painCave.errMsg, |
477 |
"LJ_FF does not support torsions.\n" ); |
478 |
painCave.isFatal = 1; |
479 |
simError(); |
480 |
} |
481 |
#ifdef IS_MPI |
482 |
MPIcheckPoint(); |
483 |
#endif // is_mpi |
484 |
|
485 |
} |
486 |
|
487 |
|
488 |
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
489 |
|
490 |
int foundText = 0; |
491 |
char* the_token; |
492 |
|
493 |
rewind( frcFile ); |
494 |
lineNum = 0; |
495 |
|
496 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
497 |
lineNum++; |
498 |
if( eof_test == NULL ){ |
499 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
500 |
" file is empty.\n", |
501 |
searchOwner ); |
502 |
painCave.isFatal = 1; |
503 |
simError(); |
504 |
} |
505 |
|
506 |
|
507 |
while( !foundText ){ |
508 |
while( eof_test != NULL && readLine[0] != '#' ){ |
509 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
510 |
lineNum++; |
511 |
} |
512 |
if( eof_test == NULL ){ |
513 |
sprintf( painCave.errMsg, |
514 |
"Error fast forwarding force file for %s at " |
515 |
"line %d: file ended unexpectedly.\n", |
516 |
searchOwner, |
517 |
lineNum ); |
518 |
painCave.isFatal = 1; |
519 |
simError(); |
520 |
} |
521 |
|
522 |
the_token = strtok( readLine, " ,;\t#\n" ); |
523 |
foundText = !strcmp( stopText, the_token ); |
524 |
|
525 |
if( !foundText ){ |
526 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
527 |
lineNum++; |
528 |
|
529 |
if( eof_test == NULL ){ |
530 |
sprintf( painCave.errMsg, |
531 |
"Error fast forwarding force file for %s at " |
532 |
"line %d: file ended unexpectedly.\n", |
533 |
searchOwner, |
534 |
lineNum ); |
535 |
painCave.isFatal = 1; |
536 |
simError(); |
537 |
} |
538 |
} |
539 |
} |
540 |
} |
541 |
|
542 |
|
543 |
|
544 |
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ){ |
545 |
|
546 |
char* the_token; |
547 |
|
548 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
549 |
if( the_token != NULL ){ |
550 |
|
551 |
strcpy( info.name, the_token ); |
552 |
|
553 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
554 |
sprintf( painCave.errMsg, |
555 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
556 |
painCave.isFatal = 1; |
557 |
simError(); |
558 |
} |
559 |
|
560 |
info.mass = atof( the_token ); |
561 |
|
562 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
563 |
sprintf( painCave.errMsg, |
564 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
565 |
painCave.isFatal = 1; |
566 |
simError(); |
567 |
} |
568 |
|
569 |
info.epslon = atof( the_token ); |
570 |
|
571 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
572 |
sprintf( painCave.errMsg, |
573 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
574 |
painCave.isFatal = 1; |
575 |
simError(); |
576 |
} |
577 |
|
578 |
info.sigma = atof( the_token ); |
579 |
|
580 |
return 1; |
581 |
} |
582 |
else return 0; |
583 |
} |
584 |
|
585 |
|
586 |
void LJ_FF::doForces( void ){ |
587 |
|
588 |
int i; |
589 |
double* frc; |
590 |
double* pos; |
591 |
double potE; |
592 |
short int calcPot = 0; |
593 |
|
594 |
// forces are zeroed here, before any are acumulated. |
595 |
// NOTE: do not rezero the forces in Fortran. |
596 |
|
597 |
for(i=0; i<entry_plug->n_atoms; i++){ |
598 |
entry_plug->atoms[i]->zeroForces(); |
599 |
} |
600 |
|
601 |
frc = Atom::getFrcArray(); |
602 |
pos = Atom::getPosArray(); |
603 |
|
604 |
doLJfortran( pos, frc, potE, calcPot ); |
605 |
} |
606 |
|